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remove mom/dad/kid cmd line arguments that were needed for mendelian walker; now we can use generic track binding!! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@389 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-04-14 00:45:34 +00:00
parent f838a5e511
commit 8e6093d5a5
1 changed files with 1 additions and 14 deletions
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15
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -53,12 +53,7 @@ public class GenomeAnalysisTK extends CommandLineProgram {
public String DOWNSAMPLE_COVERAGE = null; public String DOWNSAMPLE_COVERAGE = null;
public String INTERVALS_FILE = null; public String INTERVALS_FILE = null;
// added for mendelian walker.
//TODO: when walkers can ask for their tracks this should be removed!
public String MOTHER_GENOTYPE_FILE = null;
public String FATHER_GENOTYPE_FILE = null;
public String DAUGHTER_GENOTYPE_FILE = null;
// our walker manager // our walker manager
private WalkerManager walkerManager = null; private WalkerManager walkerManager = null;
@ -137,10 +132,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
m_parser.addOptionalArg("numthreads", "nt", "How many threads should be allocated to running this analysis.", "numThreads"); m_parser.addOptionalArg("numthreads", "nt", "How many threads should be allocated to running this analysis.", "numThreads");
m_parser.addOptionalFlag("enablethreading", "et", "Enable experimental threading support.", "ENABLE_THREADING"); m_parser.addOptionalFlag("enablethreading", "et", "Enable experimental threading support.", "ENABLE_THREADING");
//TODO: remove when walkers can ask for tracks
m_parser.addOptionalArg("mother", "MOM", "Mother's genotype (SAM pileup)", "MOTHER_GENOTYPE_FILE");
m_parser.addOptionalArg("father", "DAD", "Father's genotype (SAM pileup)", "FATHER_GENOTYPE_FILE");
m_parser.addOptionalArg("daughter", "KID", "Daughter's genotype (SAM pileup)", "DAUGHTER_GENOTYPE_FILE");
// --rodBind <name> <type> <file> // --rodBind <name> <type> <file>
//m_parser.addOptionalArg("rods", "B", "Bind rod with <name> and <type> to <file>", "ROD_BINDINGS"); //m_parser.addOptionalArg("rods", "B", "Bind rod with <name> and <type> to <file>", "ROD_BINDINGS");
@ -214,10 +205,6 @@ public class GenomeAnalysisTK extends CommandLineProgram {
if ( DBSNP_FILE != null ) bindConvenienceRods("dbSNP", "dbsnp", DBSNP_FILE); if ( DBSNP_FILE != null ) bindConvenienceRods("dbSNP", "dbsnp", DBSNP_FILE);
if ( HAPMAP_FILE != null ) bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", HAPMAP_FILE); if ( HAPMAP_FILE != null ) bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", HAPMAP_FILE);
if ( HAPMAP_CHIP_FILE != null ) bindConvenienceRods("hapmap-chip", "GFF", HAPMAP_CHIP_FILE); if ( HAPMAP_CHIP_FILE != null ) bindConvenienceRods("hapmap-chip", "GFF", HAPMAP_CHIP_FILE);
//TODO: remove when walkers can ask for tracks
if ( MOTHER_GENOTYPE_FILE != null ) bindConvenienceRods("mother", "SAMPileup", MOTHER_GENOTYPE_FILE);
if ( FATHER_GENOTYPE_FILE != null ) bindConvenienceRods("father", "SAMPileup", FATHER_GENOTYPE_FILE);
if ( DAUGHTER_GENOTYPE_FILE != null ) bindConvenienceRods("daughter", "SAMPileup", DAUGHTER_GENOTYPE_FILE);
ReferenceOrderedData.parseBindings(logger, ROD_BINDINGS, rods); ReferenceOrderedData.parseBindings(logger, ROD_BINDINGS, rods);